49 citations · 137 across the 12 of their papers we have counts for
9 papers · 1 filter
Topological analysis reveals multiple pathways in molecular dynamics
Luca Donati, Surahit Chewle, Dominik St. Pierre +2
Molecular Dynamics simulations are essential tools for understanding the dynamic behavior of biomolecules, yet extracting meaningful molecular pathways from these simulations remai…
The Kramers turnover in terms of a macro-state projection on phase space
Luca Donati, Christof Schutte, Marcus Weber
We have investigated how Langevin dynamics is affected by the friction coefficient using the novel algorithm ISOKANN, which combines the transfer operator approach with modern mach…
Accuracy of reaction coordinate based rate theories for modelling chemical reactions: insights from the thermal isomerization in retinal
Simon Ghysbrecht, Luca Donati, Bettina G. Keller
Modern potential energy surfaces have shifted attention to molecular simulations of chemical reactions. While various methods can estimate rate constants for conformational transit…
Tensor-SqRA: Modeling the Transition Rates of Interacting Molecular Systems in terms of Potential Energies
Alexander Sikorski, Amir Niknejad, Marcus Weber +1
Estimating the rate of rare conformational changes in molecular systems is one of the goals of Molecular Dynamics simulations. In the past decades, a lot of progress has been done…
Efficient Estimation of Transition Rates as Functions of pH
Luca Donati, Marcus Weber
Extracting the kinetic properties of a system whose dynamics depend on the pH of the environment with which it exchanges energy and atoms requires sampling the Grand Canonical Ense…
A review of Girsanov Reweighting and of Square Root Approximation for building molecular Markov State Models
Luca Donati, Marcus Weber, Bettina G. Keller
Dynamical reweighting methods permit to estimate kinetic observables of a stochastic process governed by a target potential from trajectories that have been generate…
Assessing transition rates as functions of environmental variables
Luca Donati, Marcus Weber
We present a method to estimate the transition rates of molecular systems under different environmental conditions which cause the formation or the breaking of bonds and require th…
Markov models from the Square Root Approximation of the Fokker-Planck equation: calculating the grid-dependent flux
Luca Donati, Marcus Weber, Bettina G. Keller
Molecular dynamics are extremely complex, yet understanding the slow components of their dynamics is essential to understanding their macroscopic properties. To achieve this, one m…
Dynamical reweighting methods for Markov models
Stefanie Kieninger, Luca Donati, Bettina G. Keller
Markov State Models (MSM) are widely used to elucidate dynamic properties of molecular systems from unbiased Molecular Dynamics (MD). However, the implementation of reweighting sch…